Technical Abstract:
In 1999, the USDA-ARS in collaboration with Mars Incorporated initiated a project to apply modern molecular genetic techniques to cacao breeding. The objective was to develop an international Marker Assisted Selection (MAS) breeding program focusing on disease resistance. Mapping populations were produced, molecular markers developed and quantitative trait loci (QTLs) identified for the major diseases. However, the low density linkage maps (400-500 SSR markers) and the small number of individuals in the mapping populations proved problematic for using the markers flanking QTLs for MAS. A complete genome sequencing project was initiated in 2008 and completed in 2010 using the cultivar Matina 1-6. The sequence of the leaf transcriptome from additional cultivars from the ten previously identified genetic groups lead to the development of a 9,000 Illumina Infinium chip. Using the SNP markers, greater saturation was achieved and this has allowed us to reduce the size of the QTLs and to identify candidate genes within these flanking regions. New QTLs have been identified for Vascular Streak Dieback and Black Pod resistance, flavor characteristics, flavanols and agronomic traits. The highly saturated genetic maps, together with the high quality reference sequence form Matina 1-6 and the genetic analysis strategies we have developed , have allowed us to identify the actual genes regulating traits in cacao including the genes regulating pod color which will be discussed.